Site-specific recombination plays an important role in a number of genetic processes such as phage integration, control of gene expression, and as part of the transposition process. In bacteria, site-specific recombination can control expression of surface antigens and promote spread of antibiotic resistance gene thru transposition. We have devised a genetic screening assay for the identification of inhibitors of site-specific recombination mediated by the TN3 resolvase. Using this rapid screening procedure we have screened over 6,000 compounds, and have discovered 26 potential inhibitors in vivo 5 of these 26 compounds will inhibit site-specific recombination in vitro using purified TN3 resolvase. The goals of this research are to discover the mechanism by which these inhibitors act, and to determine if they will inhibit other, related site-specific recombination systems. Because the TN3 resolvase represses itself as well as mediate site-specific recombination, we will separate these two functions by cloning the tnpR under different promoters. This will allow in vivo studies on inhibition of recombination to proceed without side effects on resolvase levels. Mutants resistant to inhibition will also be isolated. The binding of the inhibitors to the resolvase protein will be measured. The step in the recombination reaction that is blocked by the inhibitors will be determined and the structure of any intermediates will be elucidated. We will also test these inhibitors on phase variation in Salmonella and Mu G-loop switching, both of which involve site-specific recombination by proteins related to TN3 resolvase.